I am using the newest version, 0.3, and I am pretty much stuck exactly where you are, I am getting the same NXT not found message. I was hoping you would share what you did to solve the problem. Thanks.

Nevermind on that one, I simply needed to load the firmware for 0.3 using the command nxjflash and follow different steps for compiling and uploading the program that are new to 0.3. I am learning as I go and will probably post my own tutorial that uses 0.3 in the future.